Rev Language Reference


clade - Clade

A clade is a subtree within a phylogeny.

Usage

clade(String ..., String[] ..., Clade ..., Taxon ..., Taxon[] ..., RealPos age, Natural missing, Bool negative, Bool optional_match)

Arguments

... : String (pass by const reference)
Taxon names as string values.
... : String[] (pass by const reference)
Taxon names as a vector of string values.
... : Clade (pass by const reference)
Taxa as clade objects.
... : Taxon (pass by const reference)
Taxon names as taxon values
... : Taxon[] (pass by const reference)
Taxon names as a vector of taxons
age : RealPos (pass by value)
The age of the clade (optional).
Default : NULL
missing : Natural (pass by value)
Number of missing taxa in the clade (optional).
Default : NULL
negative : Bool (pass by value)
Is this a negative clade constraint?
Default : FALSE
optional_match : Bool (pass by value)
Clade constraint satisfied when any Clade argument matched
Default : FALSE

Details

Clades are defined in terms of a taxon set and a shared tree topology. In phylogenetic analyses, clades are generally used (a) to constrain tree topologies to match provided taxon relationships, (b) to identify the most recent common ancestor of a taxon set within a phylogeny, or (c) to apply node age calibrations on particular nodes in the phylogeny.

Example

# read in a tree
phy = readTrees("primates.tre")[1]
# get taxa from the tree
taxa = phy.taxa()
# create a clade for (1,2) using taxon objects
clade_12 = clade( taxa[1], taxa[2] )
# create a clade for (1,2,3)
clade_123 = clade( taxa[3], clade_12 )
# create a clade for (4,5) using taxon names
clade_45 = clade( "Taxon_4", "Taxon_5" )
# create a negative clade constraint
clade_not_23 = clade( taxa[2], taxa[3], negative=true )
# create an optional clade constraint
clade_67 = clade( taxa[6], taxa[7] )
clade_68 = clade( taxa[6], taxa[8] )
clade_67_or_68 = clade( clade_67, clade_68, optional_match=true )

Methods

  • getAge()
  • getNumberOfTaxaMissing()
  • getTaxon(Natural node)
  • getTaxonName(Natural node)
  • setAge(RealPos a)
  • setNumberOfTaxaMissing(Natural n)
  • size()

See Also